


What Remains

by A_Modern_Girl



Series: What Remains [2]
Category: Star Trek: Voyager
Genre: Angst, Chakotay needs therapy, F/M, Hopeful Ending, Janeway needs therapy, Post-Endgame, they all need therapy tbh
Language: English
Status: Completed
Published: 2020-07-04
Updated: 2020-07-04
Packaged: 2021-03-04 23:21:49
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 3,742
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/25074550
Author URL: https://archiveofourown.org/users/A_Modern_Girl/pseuds/A_Modern_Girl
Summary: Chakotay’s celebration of Voyager’s return to the Alpha Quadrant is cut short when he discovers that Captain Janeway is missing.
Relationships: Chakotay/Kathryn Janeway
Series: What Remains [2]
Series URL: https://archiveofourown.org/series/1815967
Comments: 12
Kudos: 55





	1. Chapter 1

**Author's Note:**

> This is the sequel/companion of The Weekend, although they can be read in any order. No mention of C/7 because our heroes have bigger problems to deal with. All mistakes are mine.

Chakotay disembarked the transport ship into a cold, misty morning in San Francisco. While the other passengers shivered and drew their jackets closer, Chakotay took a deep breath and savored the moist air. He reflexively reached for his commbadge, but caught himself and lowered his arm. He didn’t have to do a comm check in the heart of friendly territory.

All Voyager crewmen not based on Earth had been given a month’s leave before their debriefings. No officer was exempt, no matter how senior. Chakotay fought to stay, to help Kathryn through her debriefings, but he was politely rebuffed. The mandatory leave served a practical purpose - after the Dominion War, there were only so many qualified staff available to take their statements. Sending the non-Terrans home allowed Starfleet Command to pace themselves.

Once he understood their reasoning, he embraced the opportunity to see his family on Dorvan. His sister made him feel right at home, despite the long absence. The desert heat and the support of his family nourished and restored him, but he knew that world was not where he belonged. Duty was calling to him again.

San Francisco was not Chakotay’s favorite place on Earth, but he was just as happy to be there as the day he started at Starfleet Academy. Just like that day, decades ago, the possibilities in front of him were both daunting and exciting. Reliable sources had hinted that he would be offered command of his own Starfleet ship. It would fulfill one of his oldest dreams, one that he had given up on more than once.

Still, an Earth-based assignment also had its appeal. There was challenging work to be done, with the benefit of weekends which could be filled with hiking, barbeques, and concerts. Chakotay listened as the breeze rustled the branches above him and closed his eyes appreciatively. Despite the weeks he spent on Dorvan, being on a planet was still more alien to him than the vastness of space. Would it be so bad to explore a new kind of life and defer his dream a little longer?

Chakotay let his thoughts run amok as he crossed the Starfleet grounds to his apartment. He keyed in his door code and walked into the unfamiliar space. There had been so many debriefings and functions to attend after Voyager’s return that he hadn’t yet unpacked his belongings. His quarters on Voyager had been much more homely. He would have to fix that as soon as possible.

First, he opened his bag and carefully extracted the roses he had brought back from his sister’s garden and put them in water. Second, he sat down to his terminal to craft a message to Kathryn. It was Saturday afternoon, and if he knew her at all, she was probably working over the weekend.

 _I’m back from Dorvan,_ he typed, _Dinner soon? I missed you._

He hit send before he could reconsider his confession, and he felt his stomach do a summersault. When there was no immediate reply to his message, he forced himself to get up from the screen and unpack. If he got the place straightened up, he could cook for Kathryn that evening, he reasoned. The possibility made him smile.

As he sorted his belongings, he thought about the last time he had seen her. They had only been on Earth for a week before leave was announced for non-Terrans. While he hastily made travel plans, Janeway managed to organize a farewell gathering in an old gymnasium at the Academy. Chakotay didn’t know how she managed to keep the press and the admiralty away, but her efforts yielded a wonderful and intimate celebration. 

He could still clearly see Mike Ayala dancing with his daughter at last. He had tried to commit Naomi’s joyful laugh to memory as he swung her around the dance floor beside them. His transport was scheduled to leave at midnight, so he made his goodbyes while the party was still in full swing. He managed to talk to almost everyone, but whenever he tried to bid Kathryn farewell, she was always busy talking to other crewmen. 

He waited as long as he could, but trips to Dorvan were rare, and missing his transport was a risk he couldn’t take. Reluctantly, he had hefted his bag and set off across campus towards the launch pad. It was a quiet night on the Starfeet grounds, and he started when he heard rapid footfalls behind him. It was Kathryn, heels dangling in one hand, running to catch up.

“Hey,” she said breathlessly, “Can I walk you to the station?”

“Sure,” he replied, too surprised to think of something better to say.

Chakotay’s heart skipped a beat when she looped her arm through his.

“The party was wonderful,” he offered, “Neelix would be proud.”

He could sense her smile in the dark. “He would, wouldn’t he?”

Instead of traditional streetlights, the path itself was gently illuminated. Whether it was nanotechnology or some form of algae, Chakotay couldn’t be sure, but it bathed their surroundings in a soft glow. It gave the evening a magical quality, and combined with his anticipation for his trip, made him feel like anything was possible.

Too soon the launchpad was in sight, and Chakotay’s eyes adjusted to the brightness. What should he say to Kathryn? A ‘thank you’ seemed too little, a ‘goodbye’ was too final. His mind raced, but nothing came. Luckily, she spared him the decision by yanking on his arm.

“Chakotay,” she started.

It was a tone of voice he knew well - there was a speech coming. “Yes?”

“I wasn’t always fair to you in the Delta Quadrant.” Chakotay watched, fascinated, as she swallowed and coughed. “I wasn’t always good to you, either. You have been my dearest friend, and you don’t owe me a thing. But, if you are willing to explore what we could be together… I want you to know I’m ready to try.”

“Kathryn…” Chakotay stuttered.

“Don’t make a decision now,” she said quickly, “Think about it while you’re on Dorvan. I’ll be here when you get back.”

Chakotay was robbed of any remaining sense when Kathryn kissed him on the cheek and disappeared into the dark. He watched her silhouette dart back down the path, still trying to understand what had happened. A warning blared - five minutes to take off. Chakotay hurried aboard and found his cabin. Kathryn had given him a whole month to make a decision, but he knew his answer even before his ship left orbit. He didn’t know what life had in store for him, but he wanted to find out with Kathryn.

Chakotay was smiling to himself, enjoying the memory, when the terminal finally pinged. He practically bounced off the wall where he was hanging a picture to check it. His shoulders slumped when he realized it wasn’t Kathryn, but B’Elanna, inviting him to brunch the next morning. He swallowed his disappointment and smiled. It wasn’t the call he had been waiting for, but it was certainly still welcome. He punched in his acceptance, and then, checking the time, resigned himself to dinner alone.


	2. Chapter 2

The next morning dawned clear and beautiful, and Chakotay couldn’t help but smile at the greenery around him. The desert of Dorvan would always be special to him, but he admired the cedar and oak trees all the same. The Paris-Torres family was only a few blocks away, so he didn’t have to worry about being late. Chakotay had barely knocked before B’Elanna burst out of the front door and wrapped him in a tight hug.

“How was the trip?” she asked, leading him inside.

“Fantastic,” he replied, “Apparently, I’m the fun uncle, even if I am a bit contrary.”

B’Elanna’s response was interrupted by a happy shriek from the back of the house.

“Come on,” B’Elanna urged with a tired smile, “Sounds like Miral is hungry.”

Brunch lasted until almost two in the afternoon. It was amazing how long it took to share a month’s worth of stories with people he was used to seeing everyday. Interruptions from Miral didn’t help on that front, but Chakotay was thrilled to see how big she was, and how happy and alert. Only one thing was bothering him. It had been almost a full day since he sent his message, but Chakotay still hadn’t heard from Kathryn.

“Have you seen Captain Janeway lately?” Chakotay asked Tom on his way out.

“We were hoping she’d be able to join us today, actually,” Tom said with a wink, “But my dad says she’s out on assignment.”

“Assignment?” Chakotay repeated.

He was so intrigued by the second part of Tom’s statement that he was willing to ignore the cheekiness of the first half. Apparently she was working, as Chakotay had suspected. But what kind of assignment required her attention all weekend?

Tom shrugged, “He said she would be back soon, but he didn’t know when.”

“She’s off-world?” Chakotay asked.

Tom shrugged again, “I don’t know, but I’ll let you know if I hear anything.”

Chakotay thanked him and walked back out into the beautiful day. It was perfect weather for a walk, so he treated himself to a tour of his surroundings. He had never paid much attention to San Francisco as a young cadet or junior officer, but now he savored the sights and sounds of the modern city. Every time he caught a whiff of coffee, he looked around for Kathryn, but she was nowhere in sight.

The next few days passed pleasantly enough. Chakotay joined the Ayalas for a hike near their home in Oregon. He met with a few of the professors at the academy to learn more about becoming an instructor. But no matter how he distracted himself, his thoughts were always on Kathryn. Every day when he returned home, the first thing he did was check his messages, but still there was no reply.

He brooded as he ate dinner alone yet again. What would take Kathryn out of comm range for so long? It seemed that Admiral Paris was in the loop - maybe he would be willing to share information with a more senior officer than Tom. It seemed implausible, but he had to try. Chakotay sat down at his console and keyed in a meeting request for the Admiral. Despite the late hour, it was quickly accepted for the next day. Finally, he was on his way to finding out what was going on.

The next morning, Chakotay donned his uniform for the meeting. It was the new gray on black design that he was still getting used to. He took a few extra moments to make sure his pips were straight - no more provisional rank bar for him. Confident in his appearance, he set off for the Admiral’s office. He was shown in immediately, which he took as a good sign.

“Admiral, thank you for seeing me,” Chakotay said, extending his hand.

Admiral Paris gave him a kind smile. He asked after Chakotay’s trip home and future plans. Without intending to, Chakotay soon found himself in the middle of a detailed discussion of the different ships he could command. Chakotay was surprised and flattered that the admiral had taken such an interest in him. Gently, he tried to steer the conversation back towards the purpose of his visit.

“I would love to see you leading one of our anti-piracy squadrons,” Admiral Paris said, “Your tactical know-how would be a huge advantage.”

“It’s something I’ll have to consider sir, thank you,” Chakotay replied, “But actually, I was here to discuss something a little different.”

“Oh?”

“It’s Captain Janeway, sir. I haven’t been able to reach her since I got back, and Tom told me she was on assignment. I was hoping you could tell me more.”

“Well, I can confirm what Tom said,” he answered, looking uneasy for the first time since their conversation began, “but I’m afraid that that’s all I can say.”

“We haven’t even been back two months,” Chakotay protested, “she shouldn’t be on any kind of mission, let alone one you can’t tell me about. She’s been through more than all of us. Surely, you can understand that.”

“Chakotay, I’ve been a first officer myself. I know you want to look after her, but Captain Janeway isn’t your captain anymore. You’re in separate chains of command, and her assignment is not your business.” 

“Sir, with all due respect, Captain Janeway will always be more than a fellow officer to me,” Chakotay said softly, “I just need to know she’s all right.”

Admiral Paris gave him a long look and sighed. “As it happens, I have a secure comm channel open with her. I’ll let her know you’re trying to get in touch.”

It wasn’t the reassurance he had hoped for, but Chakotay could tell it was the best he was going to get. In the tactical part of his brain, he noted that if there was an open comm, she was still in the sector - friendly territory. It was a good hint, at least.

“Thank you Admiral, I really appreciate it,” Chakotay said, extending his hand.

Admiral Paris shook it firmly. He implored Chakotay once more not to worry about Kathryn, and to focus instead on finding his path. The admiral meant well, but Chakotay knew that was advice he couldn’t follow. He thought of all the terrible things Kathryn had gone through in the last year alone. She had been abducted not once but twice, and had barely survived her encounter with the dark matter creatures. Kathryn had been through enough. If Starfleet couldn’t see that, Chakotay would have to protect her himself.

On the walk back to his quarters, he considered his options. Certainly, Seven could hack into Starfleet Command and figure out what Kathryn’s orders were. For a more subtle approach, Chakotay could trace Admiral Paris’ comm lines if Harry Kim helped him. Either of them would be happy to assist if they thought Janeway was in danger. But was it worth the risk? What if he was wrong?

There was an alert on his terminal when he walked in - one new message. Chakotay’s heart leapt when he saw it was Kathryn at last.

_Admiral Paris said you were looking for me. Can you meet me for lunch tomorrow?_

The message was only two minutes old. He quickly confirmed and waited for details. The response was almost instantaneous.

_Great, see you at 1300._

There were coordinates at the end of the message, and Chakotay frantically plugged them in. Jupiter station? That was where Starfleet's most promising research projects were developed. What was she doing there? Chakotay straightened his shoulders and sighed. He would find out in 24 hours. He just had to be patient for one more day.


	3. Chapter 3

Chakotay arrived on Jupiter Station at 1255. He had decided to wear his uniform to better blend in. The tactical, pessimistic part of his brain was still planning an extraction, even though he was trying to keep an open mind. He saw a hint of auburn hair in the crowd, and then suddenly Kathryn was right in front of him, beaming from ear to ear.

The transporter room was full at the lunch hour, and neither of them seemed sure how to greet the other. Chakotay somehow ended up clasping both of Kathryn’s hands in his as he returned her smile. She tugged on his hands and led him away from the crowd. Chakotay had so many questions, but he restrained himself until they entered her personal quarters. The view of Jupiter’s red eye was astonishing, but Chakotay barely noticed.

“It’s so good to see you Kathryn. When you weren’t on Earth when I got back, I got worried. I can’t believe you buried yourself in research already,” he said with a chuckle.

Kathryn gave him a quizzical look. Lunch was set up already at a table under the viewport, and she indicated for him to join her there. She set her napkin in her lap, and then looked up into his eyes. “What do you think I’m doing up here, Chakotay?”

Chakotay found himself in unexpected territory. “The admiral couldn’t tell me what your mission was, but clearly, if you’re up here it has to be top-secret research.” He scanned her face. “Right?

“Chakotay, I’m not on a mission,” she answered, softly, “I’m not doing research. I’m a patient.”

Chakotay tried to process this revelation and form a cohesive response, but the best he could do was, “A patient? Are you… all right?”

“I’m doing much better, thank you, “ she replied with an indulgent grin, “The Doctor and I are borrowing some of Professor Zimmerman’s lab space to work on my mental health. It’s a journey, but I’m making progress.”

“A journey?” he parroted.

Kathryn nodded. “We’re unpacking my experience on Voyager. It’s slow, and some days are very, very hard. We mourn the dead. I go on angry tirades for hours. Some days, I can’t talk at all. The important thing is making sense of what happened, so I can move forward.”

“But,” Chakotay said, taking her hands across the table, “Why Jupiter Station?”

Kathryn sighed, and looked out the viewport at the swirling gases below. Chakotay was tempted to retract his question, even as he hoped she would answer. What could keep her from Earth, after working for so long to get there? Finally, Kathryn squeezed his hands.

“Everything was fine at first,” Kathryn shook her head ruefully, “I didn’t see it at the time, but as everyone was crying and holding their loved ones, they were processing what had happened, but I wasn’t. The debriefings were going so well. I never got angry when the admirals asked their probing questions or disagreed with my decisions. That should have been a warning sign all in itself.”

Chakotay nodded while he mentally kicked himself. If he had been there, he would have noticed. He would have confronted her. Guilt crept into his belly even as he focused on her story.

“But something changed,” he prodded gently.

Kathryn took a deep breath before continuing. “One evening, I was at my mother’s house in Indiana. We had just finished dinner, and I was doing dishes in the kitchen. I looked out the window and there were real corn fields that stretched as far as the eye could see. I knew I could walk all day and not see the shimmering pixels of a hologrid. The dishwater on my hands had come from a well in the ground, not a replicator or a recycler. It was suddenly all too real.”

“I felt something like that on Dorvan,” Chakotay offered, “I’d look out at the horizon, or smell my sister’s cooking, and suddenly feel dizzy.”

“In my case, I started crying, and no matter how hard I tried, I couldn’t stop. My mother called the Doctor, who called Admiral Paris, and they had me brought here,” she said.

“I’m so sorry,” Chakotay said sincerely, “I should have been here-”

“Chakotay stop it,” she interrupted, “You are a wonderful friend. You supported me through seven long, hard years in the Delta Quadrant. But this was a different challenge, and to face it, I needed professional help. Don’t you dare think otherwise.”

“I know,” he replied, “but a part of me still wishes you didn’t have to go through this. Not after everything else.”

Kathryn gave him a small smile, and then unexpectedly changed the topic.

“I dropped quite a bomb on you right before you left,” Kathryn said.

“I remember,” Chakotay replied, blushing.

“My interest hasn’t changed.” Her voice trembled slightly. “But my priorities have. I need some time.”

“Take all the time you need,” Chakotay answered immediately, “Whether you need space, or a friend, just know that I will help in any way I can.”

“Given that you’ve crossed the solar system on less than a day’s notice, I believe you,” she said.

Chakotay paused, and reflected on his actions since he had gotten back. While Tom had seemed surprised that Kathryn had an assignment, he was the one who had leapt to conclusions and interrogated the admiral. He shook his head.

“What’s wrong?” Kathryn asked.

“When I didn’t know where you were, my first instinct was that you were in danger. Even when Admiral Paris said you were fine, I didn’t believe him until I actually saw you. I’m afraid I gave him a bit of a hard time.”

“Hey, it wasn’t right for Owen to tell you I was on a mission while I was up here. If the situation had been reversed, I would have been worried about you too,” she argued.

“I know, but I would have broken every rule in the book for you. I could have ruined both our careers,” he replied.

“Hmmm,” Kathryn paused, “Well, maybe we can fix that at least. When you get back, can you work with Owen to adjust the story? It’s okay if the crew knows that I’m… recovering. But let’s leave it at that.”

Chakotay nodded decisively, “I’ll let him know when I get back. I want to go see him anyway, to apologize for my behavior.”

"If it makes you feel better, I am glad I got to see you. I missed you, Chakotay."

“It does, believe me,” he said, blushing again, “And so you know, I’m going to talk to my counselor when I get back. If we are going to see each other, I’m going to have to learn how to support you even when I can’t be there to protect you.”

“I think that sounds like a great idea,” Kathryn said. She seemed to finally notice the food they had left untouched. Chakotay noticed it too, and his mouth watered. Their discussion has completely captivated him, but now that it was winding down, he realized he was famished. Still, there was one last order of business he needed to attend to.

He raised his glass, “To new beginnings.”

Kathryn beamed at him, “To new beginnings.”

When Chakotay returned to Earth that afternoon, he fulfilled his promises to Kathryn by calling both Admiral Paris and his counselor. With those items complete, he sat back and smiled. He would never regret his time on Voyager, not for an instant. But it was time to put that journey in the past, and embark on the new, wonderful path in front of him.

**Notes for the Chapter:**

> The title of this work and the series comes from the song Remains by Maurissa Tancharoen & Jed Whedon. If you enjoyed this story, go give it a listen! Thanks for reading.


End file.
